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Exomiser 13.1.0, Protocol B (Yuan et al. 2024)

Exomiser 13.1.0, Protocol B: REVEL and MVP pathogenicity sources; singleton.

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Evaluations and results

2 evaluations · 14 results. Different protocols are not a single leaderboard.

Sorted by Top-1 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	Top-1 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)	Top-10 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)	Top-20 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)	Top-30 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)	Top-40 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)	Top-5 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)	Top-50 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)
Exomiser 13.1.0, Protocol B (Yuan et al. 2024)Evaluation	Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1), DDD 305 solved probands (Yuan et al. selection)	53.1% (best in column)	87.9% (best in column)	91.8% (best in column)	94.1% (best in column)	94.8% (best in column)	83.3% (best in column)	95.7% (best in column)
Exomiser 13.1.0, Protocol B (Yuan et al. 2024)Evaluation	Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1), KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	48%	82.2%	86.8%	90.1%	92.1%	76.3%	92.8%

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Exomiser 13.1.0, Protocol B (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	53.1% Top-1 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser Protocol B on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, Exomiser, PROT B), column 'Top1 (%)'
Configuration: Exomiser 13.1.0, Protocol B (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	87.9% Top-10 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser Protocol B on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, Exomiser, PROT B), column 'Top10 (%)'
Configuration: Exomiser 13.1.0, Protocol B (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	91.8% Top-20 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser Protocol B on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, Exomiser, PROT B), column 'Top20 (%)'
Configuration: Exomiser 13.1.0, Protocol B (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	94.1% Top-30 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser Protocol B on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, Exomiser, PROT B), column 'Top30 (%)'
Configuration: Exomiser 13.1.0, Protocol B (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	94.8% Top-40 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser Protocol B on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, Exomiser, PROT B), column 'Top40 (%)'
Configuration: Exomiser 13.1.0, Protocol B (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	83.3% Top-5 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser Protocol B on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, Exomiser, PROT B), column 'Top5 (%)'
Configuration: Exomiser 13.1.0, Protocol B (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	95.7% Top-50 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser Protocol B on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, Exomiser, PROT B), column 'Top50 (%)'
Configuration: Exomiser 13.1.0, Protocol B (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	48% Top-1 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser Protocol B on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, Exomiser, PROT B), column 'Top1 (%)'
Configuration: Exomiser 13.1.0, Protocol B (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	82.2% Top-10 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser Protocol B on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, Exomiser, PROT B), column 'Top10 (%)'
Configuration: Exomiser 13.1.0, Protocol B (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	86.8% Top-20 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser Protocol B on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, Exomiser, PROT B), column 'Top20 (%)'
Configuration: Exomiser 13.1.0, Protocol B (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	90.1% Top-30 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser Protocol B on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, Exomiser, PROT B), column 'Top30 (%)'
Configuration: Exomiser 13.1.0, Protocol B (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	92.1% Top-40 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser Protocol B on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, Exomiser, PROT B), column 'Top40 (%)'
Configuration: Exomiser 13.1.0, Protocol B (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	76.3% Top-5 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser Protocol B on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, Exomiser, PROT B), column 'Top5 (%)'
Configuration: Exomiser 13.1.0, Protocol B (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	92.8% Top-50 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Exomiser Protocol B on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, Exomiser, PROT B), column 'Top50 (%)'

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Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Original source · Scientific Reports 14:2845, published 2024-02-03; PMC10838329 full-text XML

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Technical metadata and extraction receipts

Stable ID: rare-ranking-20261009-config-yuan2024-exomiser-protocol-b

areas: dna-genomes
contexts: clinical_research
method types: conventional_pipeline
reported name: Exomiser 13.1.0, Protocol B (Yuan et al. 2024)
foundation model eligible: false
version: 13.1.0
parameters: REVEL and MVP pathogenicity sources; singleton
source locator: Table 1 rows 'Exomiser', PROT 'B'; Results 'Performance improvement assessment'
limitations: Protocol option tables are in Figure 2 (image, not read); descriptions are from the Results text, and the exact pathogenicity source in Protocols C and D is not stated in the text.
provenance note: Exomiser 13.1.0, Protocol B (Yuan et al. 2024) as evaluated in the cited comparison.

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